Fair points. But, mark-recapture is about practicality. It's not perfect, but it's a solid compromise between accuracy and feasibility (so I mean best in these regards, to be 100% clear). Sure, different methods might skew results, but this technique is about getting a reliable estimate, not pinpoint accuracy. As for learning behavior in fish, that's considered in many studies (and many other things, like listed here: https://fishbio.com/fate-chance-encounters-mark-recapture-st... ), but overall, it doesn't hugely skew the population estimates. So, again, it's about what works best in the field, not in theory.
